This is what I found when I looked into it a couple months ago, from a previous thread I wrote. I walked away from further research when I saw the difference between the heaters used in Climatronic I and Climatronic II.
I spend a few minutes last night reviewing the schematics of the 2 zone climatic and standard. I have seen control units for under $100. However, it works so well as it is, that I am not sure if it is really necessary upgrade or just a fun thing to reverse engineer. Decided to lay down until the urge goes away as I am in the gathering phase for a Infotainment MIB1 to MIB2 upgrade, and also need a break after a Lighting Package retrofit that was quite challenging.
Took another look. Need new A/C control panel, sunlight photo sensor (not used in MK6) left and right temperature sensors, and footwell sensor. The left and right temperature sensors don't look like a problem, the sunlight photo sensor is located between defroster vents and look likes my SE has location for, and the footwell sensor looks like access would be a challenge. All looks doable and a fun project. This is a DIY on a MK6
http://www.golfmk6.com/forums/showthread.php?t=42037
Did a little more digging. One potential issue is component location shows a Climatronic I (fancy name for the heater/AC box) and Climatronic II for full auto. It would take some investigation to see if the Climatronic I could be adapted similar to the MK6 retrofit of cutting a hole in port and adding footwell sensor. The three sensor are $90 new, and used control unit is $100, so this isn't a a lot of cash, but it would take some study, planning, and work.
Something else I wrote concerning:
The heater systems are Climatronic I and Climatronic II which when connected using sensors and bus lines supports the 2 zones. When I saw a couple sensors and control module with wiring it didn't look like a big deal, but when I learned about different heater units I walked away from further investigation.